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While studying the archaeological records of the now-destroyed planet Sarpeidon, a scholar aboard the USS Enterprise finds pictures of an ice-age cave painting that depicts a Vulcan face. Spock realizes that his involvement with Zarabeth in the episode "All Our Yesterdays" resulted in the birth of a child. Along with Captain Kirk and Dr. McCoy, he uses the Guardian of Forever (featured in the episode "The City on the Edge of Forever") to journey back into Sarpeidon's past and rescue his son. Due to a miscalculation, they find a young man of twenty-eight instead of a child, who tells them that his name is Zar and that his mother Zarabeth died in an accident many years before. Spock introduces himself but refuses to allow Zar to call him "Father."

Zar returns to the Enterprise and passes as a distant relative of Spock, who oversees his education and attempts to train him in Vulcan telepathic techniques. They discover that Zar is an unusually strong telepath for a Vulcan; he can establish contact without touching the other person. Zar becomes conflicted and hurt by his father's apparent refusal to acknowledge him.

The Enterprise is called back to the planet Gateway to protect the Guardian of Forever from a Romulan intelligence raid. It is imperative to the security of the United Federation of Planets that the Romulans not discover the Guardian's powers; if they cannot be driven away, Gateway must be destroyed. The Romulans place a force field around the Guardian and hide themselves behind a ground-based cloaking device. Zar volunteers to help Spock counteract the force field because he can sense whether Romulans are present even if he cannot see them. Their first try is unsuccessful, but when they rendezvous with Kirk the three men discover they are trapped on the planet while the Enterprise with Scotty in command battles the Romulans. They decide to try again, but Spock disables Zar with the Vulcan nerve pinch, wishing to spare him from danger. Kirk and Spock are captured and tortured by the Romulans. When Zar wakes up, he is able to telepathically sense their danger. He also realizes that his father cares about him, since he chose to protect Zar instead of Kirk, his closest friend. The Enterprise defeats the Romulan ships and a rescue party beams down. Zar creates a diversion by causing an explosion, allowing the others to rescue Kirk and Spock.

Once the Romulan threat is over, Zar decides to use the Guardian to return to Sarpeidon's past, but to a more settled location than the one he originally inhabited. He has discovered evidence that he is crucial to the planet's unusually rapid cultural evolution.